/*
 * Copyright (c) 2018 The Hyve B.V.
 * This code is licensed under the GNU Affero General Public License (AGPL),
 * version 3, or (at your option) any later version.
 */

/*
 * This file is part of cBioPortal.
 *
 * cBioPortal is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package org.cbioportal.legacy.web;

import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.Parameter;
import io.swagger.v3.oas.annotations.media.ArraySchema;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
import io.swagger.v3.oas.annotations.responses.ApiResponse;
import io.swagger.v3.oas.annotations.tags.Tag;
import jakarta.validation.Valid;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.cbioportal.legacy.model.StructuralVariant;
import org.cbioportal.legacy.service.StructuralVariantService;
import org.cbioportal.legacy.web.config.InternalApiTags;
import org.cbioportal.legacy.web.config.annotation.InternalApi;
import org.cbioportal.legacy.web.parameter.StructuralVariantFilter;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.validation.annotation.Validated;
import org.springframework.web.bind.annotation.RequestAttribute;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;

@InternalApi
@RestController()
@RequestMapping("/api")
@Validated
@Tag(name = InternalApiTags.STRUCTURAL_VARIANTS, description = " ")
public class StructuralVariantController {
  @Autowired private StructuralVariantService structuralVariantService;

  @PreAuthorize(
      "hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/structural-variant/fetch",
      method = RequestMethod.POST,
      consumes = MediaType.APPLICATION_JSON_VALUE,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(
      description =
          "Fetch structural variants for entrezGeneIds and molecularProfileIds or sampleMolecularIdentifiers")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content =
          @Content(
              array = @ArraySchema(schema = @Schema(implementation = StructuralVariant.class))))
  public ResponseEntity<List<StructuralVariant>> fetchStructuralVariants(
      @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface
          @RequestAttribute(required = false, value = "involvedCancerStudies")
          Collection<String> involvedCancerStudies,
      @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface
          @Valid
          @RequestAttribute(required = false, value = "interceptedStructuralVariantFilter")
          StructuralVariantFilter interceptedStructuralVariantFilter,
      @Parameter(
              required = true,
              description =
                  "List of entrezGeneIds, structural variant queries and molecularProfileIds or sampleMolecularIdentifiers")
          @Valid
          @RequestBody(required = false)
          StructuralVariantFilter structuralVariantFilter) {

    List<String> molecularProfileIds = new ArrayList<>();
    List<String> sampleIds = new ArrayList<>();

    if (interceptedStructuralVariantFilter.getSampleMolecularIdentifiers() != null) {
      interceptedStructuralVariantFilter
          .getSampleMolecularIdentifiers()
          .forEach(
              sampleMolecularIdentifier -> {
                sampleIds.add(sampleMolecularIdentifier.getSampleId());
                molecularProfileIds.add(sampleMolecularIdentifier.getMolecularProfileId());
              });
    } else {
      molecularProfileIds.addAll(interceptedStructuralVariantFilter.getMolecularProfileIds());
    }
    List<StructuralVariant> structuralVariantList =
        structuralVariantService.fetchStructuralVariants(
            molecularProfileIds,
            sampleIds,
            interceptedStructuralVariantFilter.getEntrezGeneIds(),
            interceptedStructuralVariantFilter.getStructuralVariantQueries());

    return new ResponseEntity<>(structuralVariantList, HttpStatus.OK);
  }
}
